In [1]:
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import requests
import json
import pandas as pd
import sys
sys.path.insert(0,"/home/yunye/gwaslab/gwaslab/src")
import gwaslab as gl
import requests
import json
import pandas as pd
import sys
sys.path.insert(0,"/home/yunye/gwaslab/gwaslab/src")
import gwaslab as gl
In [2]:
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In [ ]:
Copied!
In [2]:
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# Set variables object of arguments to be passed to endpoint
# Set base URL of GraphQL API endpoint
base_url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/MONDO_0004247/associations?projection=associationByEfoTrait"
# Perform POST request and check status code of response
r = requests.get(base_url)
print(r.status_code)
# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
api_response
# Set variables object of arguments to be passed to endpoint
# Set base URL of GraphQL API endpoint
base_url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/MONDO_0004247/associations?projection=associationByEfoTrait"
# Perform POST request and check status code of response
r = requests.get(base_url)
print(r.status_code)
# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
api_response
200
Out[2]:
{'_embedded': {'associations': [{'range': None,
'snps': [{'rsId': 'rs12532051',
'merged': 0,
'functionalClass': 'intron_variant',
'lastUpdateDate': '2021-06-25T04:18:22.499+0000',
'locations': [{'chromosomeName': '7',
'chromosomePosition': 148109889,
'region': {'name': '7q35'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
'templated': True}}}],
'genomicContexts': [{'isIntergenic': False,
'isUpstream': False,
'isDownstream': False,
'distance': 0,
'gene': {'geneName': 'CNTNAP2',
'entrezGeneIds': [{'entrezGeneId': '26047'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000278728'},
{'ensemblGeneId': 'ENSG00000174469'}]},
'location': {'chromosomeName': '7',
'chromosomePosition': 148109889,
'region': {'name': '7q35'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
'templated': True}}},
{'isIntergenic': False,
'isUpstream': False,
'isDownstream': False,
'distance': 0,
'gene': {'geneName': 'CNTNAP2',
'entrezGeneIds': [{'entrezGeneId': '26047'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000278728'},
{'ensemblGeneId': 'ENSG00000174469'}]},
'location': {'chromosomeName': '7',
'chromosomePosition': 148109889,
'region': {'name': '7q35'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
'templated': True}}}]}],
'loci': [{'haplotypeSnpCount': None,
'description': 'Single variant',
'strongestRiskAlleles': [{'riskAlleleName': 'rs12532051-C',
'riskFrequency': '0.96',
'genomeWide': False,
'limitedList': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12532051{?projection}',
'templated': True}}}],
'authorReportedGenes': [{'geneName': 'CNTNAP2',
'entrezGeneIds': [{'entrezGeneId': '26047'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000278728'},
{'ensemblGeneId': 'ENSG00000174469'}]}]}],
'riskFrequency': '0.96',
'study': {'initialSampleSize': '90,175 European ancestry cases, 366,152 European ancestry controls',
'gxe': False,
'gxg': False,
'snpCount': 8546065,
'qualifier': None,
'imputed': True,
'pooled': False,
'studyDesignComment': None,
'accessionId': 'GCST011500',
'fullPvalueSet': False,
'userRequested': False,
'platforms': [],
'ancestries': [{'type': 'initial',
'numberOfIndividuals': 456327,
'ancestralGroups': [{'ancestralGroup': 'European'}],
'countryOfOrigin': [{'majorArea': 'NR',
'region': 'NR',
'countryName': 'NR'}],
'countryOfRecruitment': [{'majorArea': 'Europe',
'region': 'Northern Europe',
'countryName': 'U.K.'}]}],
'diseaseTrait': {'trait': 'Gastroesophageal reflux disease, peptic ulcer disease and/or corresponding medications and treatment'},
'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
'replicationSampleSize': 'NA',
'publicationInfo': {'pubmedId': '33608531',
'publicationDate': '2021-02-19',
'publication': 'Nat Commun',
'title': 'GWAS of peptic ulcer disease implicates Helicobacter pylori infection, other gastrointestinal disorders and depression.',
'author': {'fullname': 'Wu Y', 'orcid': '0000-0002-5977-1526'}}},
'pvalueDescription': None,
'orPerCopyNum': 1.08,
'snpType': 'known',
'multiSnpHaplotype': False,
'snpInteraction': False,
'pvalueMantissa': 1,
'pvalueExponent': -9,
'standardError': None,
'pvalue': 1e-09,
'betaNum': None,
'betaUnit': None,
'betaDirection': None,
'description': None,
'_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992'},
'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992{?projection}',
'templated': True},
'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992/snps'},
'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992/backgroundEfoTraits'},
'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992/study'},
'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/79001992/efoTraits'}}},
{'range': None,
'snps': [{'rsId': 'rs9800013',
'merged': 0,
'functionalClass': 'regulatory_region_variant',
'lastUpdateDate': '2022-08-15T15:51:09.848+0000',
'locations': [{'chromosomeName': 'CHR_HSCHR5_5_CTG1',
'chromosomePosition': 541908,
'region': {'name': None},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}}],
'genomicContexts': [{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 29136,
'gene': {'geneName': 'LOC105374607',
'entrezGeneIds': [{'entrezGeneId': '105374607'}],
'ensemblGeneIds': []},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 6026,
'gene': {'geneName': 'MIR4456',
'entrezGeneIds': [{'entrezGeneId': '100616381'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000264233'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 69971,
'gene': {'geneName': 'EXOC3',
'entrezGeneIds': [{'entrezGeneId': '11336'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000180104'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 68810,
'gene': {'geneName': 'PP7080',
'entrezGeneIds': [{'entrezGeneId': '25845'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000188242'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 70432,
'gene': {'geneName': 'CEP72',
'entrezGeneIds': [{'entrezGeneId': '55722'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000112877'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 6026,
'gene': {'geneName': 'MIR4456',
'entrezGeneIds': [{'entrezGeneId': '100616381'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000264233'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 74618,
'gene': {'geneName': 'EXOC3',
'entrezGeneIds': [{'entrezGeneId': '11336'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000180104'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 61016,
'gene': {'geneName': 'SLC9A3-AS1',
'entrezGeneIds': [{'entrezGeneId': '100288152'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000225138'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 98748,
'gene': {'geneName': 'EXOC3-AS1',
'entrezGeneIds': [{'entrezGeneId': '116349'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000221990'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 17459,
'gene': {'geneName': 'SLC9A3',
'entrezGeneIds': [{'entrezGeneId': '6550'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000066230'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 70432,
'gene': {'geneName': 'CEP72',
'entrezGeneIds': [{'entrezGeneId': '55722'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000112877'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 58606,
'gene': {'geneName': 'LOC105374608',
'entrezGeneIds': [{'entrezGeneId': '105374608'}],
'ensemblGeneIds': []},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 60712,
'gene': {'geneName': 'CEP72-DT',
'entrezGeneIds': [{'entrezGeneId': '100996325'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000249650'},
{'ensemblGeneId': 'ENSG00000280978'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 68943,
'gene': {'geneName': 'PP7080',
'entrezGeneIds': [{'entrezGeneId': '25845'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000188242'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 61024,
'gene': {'geneName': 'SLC9A3-AS1',
'entrezGeneIds': [{'entrezGeneId': '100288152'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000225138'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 60261,
'gene': {'geneName': 'CEP72-DT',
'entrezGeneIds': [{'entrezGeneId': '100996325'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000249650'},
{'ensemblGeneId': 'ENSG00000280978'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 14453,
'gene': {'geneName': 'LOC107986395',
'entrezGeneIds': [{'entrezGeneId': '107986395'}],
'ensemblGeneIds': []},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 17459,
'gene': {'geneName': 'SLC9A3',
'entrezGeneIds': [{'entrezGeneId': '6550'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000066230'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 13153,
'gene': {'geneName': 'LOC105374606',
'entrezGeneIds': [{'entrezGeneId': '105374606'}],
'ensemblGeneIds': []},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 98748,
'gene': {'geneName': 'EXOC3-AS1',
'entrezGeneIds': [{'entrezGeneId': '116349'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000221990'}]},
'location': {'chromosomeName': '5',
'chromosomePosition': 541908,
'region': {'name': '5p15.33'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs9800013{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
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'_links': {'snps': [{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True},
{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}]}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 246270,
'gene': {'geneName': 'TRAPPC2P2',
'entrezGeneIds': [{'entrezGeneId': '27196'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000253124'}]},
'location': {'chromosomeName': '8',
'chromosomePosition': 71202541,
'region': {'name': '8q13.3'},
'_links': {'snps': [{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True},
{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}]}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 412170,
'gene': {'geneName': 'XKR9',
'entrezGeneIds': [{'entrezGeneId': '389668'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000221947'}]},
'location': {'chromosomeName': '8',
'chromosomePosition': 71202541,
'region': {'name': '8q13.3'},
'_links': {'snps': [{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True},
{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}]}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}}},
{'isIntergenic': False,
'isUpstream': False,
'isDownstream': False,
'distance': 0,
'gene': {'geneName': 'LOC105375894',
'entrezGeneIds': [{'entrezGeneId': '105375894'}],
'ensemblGeneIds': []},
'location': {'chromosomeName': '8',
'chromosomePosition': 71202541,
'region': {'name': '8q13.3'},
'_links': {'snps': [{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True},
{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}]}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 135906,
'gene': {'geneName': 'XKR9',
'entrezGeneIds': [{'entrezGeneId': '389668'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000221947'}]},
'location': {'chromosomeName': '8',
'chromosomePosition': 71202541,
'region': {'name': '8q13.3'},
'_links': {'snps': [{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True},
{'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}]}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}}}]}],
'loci': [{'haplotypeSnpCount': None,
'description': 'Single variant',
'strongestRiskAlleles': [{'riskAlleleName': 'rs12678747-T',
'riskFrequency': None,
'genomeWide': False,
'limitedList': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs12678747{?projection}',
'templated': True}}}],
'authorReportedGenes': []}],
'riskFrequency': 'NR',
'study': {'initialSampleSize': '235 European ancestry cases, 441 European ancestry controls',
'gxe': False,
'gxg': False,
'snpCount': 5548084,
'qualifier': None,
'imputed': True,
'pooled': False,
'studyDesignComment': None,
'accessionId': 'GCST90096798',
'fullPvalueSet': False,
'userRequested': False,
'platforms': [{'manufacturer': 'Illumina'}],
'ancestries': [{'type': 'initial',
'numberOfIndividuals': 676,
'ancestralGroups': [{'ancestralGroup': 'European'}],
'countryOfOrigin': [],
'countryOfRecruitment': [{'majorArea': 'Europe',
'region': 'Northern Europe',
'countryName': 'U.K.'}]},
{'type': 'replication',
'numberOfIndividuals': 515,
'ancestralGroups': [{'ancestralGroup': 'European'}],
'countryOfOrigin': [],
'countryOfRecruitment': [{'majorArea': 'Europe',
'region': 'Northern Europe',
'countryName': 'U.K.'}]}],
'diseaseTrait': {'trait': 'NSAID-induced peptic ulcer disease'},
'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
'replicationSampleSize': '206 European ancestry cases, 309 European ancestry controls',
'publicationInfo': {'pubmedId': '34864618',
'publicationDate': '2021-12-02',
'publication': 'EBioMedicine',
'title': 'Genome-Wide association between EYA1 and Aspirin-induced peptic ulceration.',
'author': {'fullname': 'Bourgeois S', 'orcid': None}}},
'pvalueDescription': None,
'orPerCopyNum': 2.03,
'snpType': 'novel',
'multiSnpHaplotype': False,
'snpInteraction': False,
'pvalueMantissa': 3,
'pvalueExponent': -11,
'standardError': None,
'pvalue': 3e-11,
'betaNum': None,
'betaUnit': None,
'betaDirection': None,
'description': None,
'_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575'},
'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575{?projection}',
'templated': True},
'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575/snps'},
'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575/backgroundEfoTraits'},
'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575/study'},
'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/95284575/efoTraits'}}}]},
'_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/efoTraits/MONDO_0004247/associations?projection=associationByEfoTrait'}}}
In [37]:
Copied!
for i in api_response["_embedded"]["associations"]:
#if i is dict:
print(i["snps"][0]["genomicContexts"][0].keys())
for i in api_response["_embedded"]["associations"]:
#if i is dict:
print(i["snps"][0]["genomicContexts"][0].keys())
dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links']) dict_keys(['isIntergenic', 'isUpstream', 'isDownstream', 'distance', 'gene', 'location', 'source', 'mappingMethod', 'isClosestGene', '_links'])
--------------------------------------------------------------------------- IndexError Traceback (most recent call last) <ipython-input-37-b92f79f249ee> in <module> 1 for i in api_response["_embedded"]["associations"]: 2 #if i is dict: ----> 3 print(i["snps"][0]["genomicContexts"][0].keys()) 4 IndexError: list index out of range
In [115]:
Copied!
api_response["_embedded"]["associations"]
api_response["_embedded"]["associations"]
Out[115]:
[{'range': '[1.31-1.49]',
'snps': [{'rsId': 'rs75021220',
'merged': 0,
'functionalClass': 'intergenic_variant',
'lastUpdateDate': '2021-06-24T20:23:26.532+0000',
'locations': [{'chromosomeName': '4',
'chromosomePosition': 110737238,
'region': {'name': '4q25'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
'templated': True}}}],
'genomicContexts': [{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 95115,
'gene': {'geneName': 'PITX2',
'entrezGeneIds': [{'entrezGeneId': '5308'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000164093'}]},
'location': {'chromosomeName': '4',
'chromosomePosition': 110737238,
'region': {'name': '4q25'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 57165,
'gene': {'geneName': 'LINC01438',
'entrezGeneIds': [],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000249519'}]},
'location': {'chromosomeName': '4',
'chromosomePosition': 110737238,
'region': {'name': '4q25'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 95115,
'gene': {'geneName': 'PITX2',
'entrezGeneIds': [{'entrezGeneId': '5308'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000164093'}]},
'location': {'chromosomeName': '4',
'chromosomePosition': 110737238,
'region': {'name': '4q25'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
'templated': True}}}]}],
'loci': [{'haplotypeSnpCount': None,
'description': 'Single variant',
'strongestRiskAlleles': [{'riskAlleleName': 'rs75021220-?',
'riskFrequency': None,
'genomeWide': False,
'limitedList': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs75021220{?projection}',
'templated': True}}}],
'authorReportedGenes': [{'geneName': 'PITX2',
'entrezGeneIds': [{'entrezGeneId': '5308'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000164093'}]}]}],
'riskFrequency': None,
'study': {'initialSampleSize': '602 European ancestry cases, 80,613 European ancestry controls',
'gxe': False,
'gxg': False,
'snpCount': None,
'qualifier': None,
'imputed': True,
'pooled': False,
'studyDesignComment': None,
'accessionId': 'GCST003490',
'fullPvalueSet': False,
'userRequested': False,
'platforms': [{'manufacturer': 'Affymetrix'}, {'manufacturer': 'Illumina'}],
'ancestries': [{'type': 'initial',
'numberOfIndividuals': 81215,
'ancestralGroups': [{'ancestralGroup': 'European'}],
'countryOfOrigin': [{'majorArea': 'NR',
'region': 'NR',
'countryName': 'NR'}],
'countryOfRecruitment': [{'majorArea': 'Europe',
'region': 'Western Europe',
'countryName': 'France'},
{'majorArea': 'Europe',
'region': 'Western Europe',
'countryName': 'Netherlands'},
{'majorArea': 'Europe',
'region': 'Northern Europe',
'countryName': 'Sweden'},
{'majorArea': 'Northern America',
'region': None,
'countryName': 'U.S.'}]},
{'type': 'replication',
'numberOfIndividuals': 19094,
'ancestralGroups': [{'ancestralGroup': 'European'}],
'countryOfOrigin': [{'majorArea': 'NR',
'region': 'NR',
'countryName': 'NR'}],
'countryOfRecruitment': [{'majorArea': 'Northern America',
'region': None,
'countryName': 'U.S.'},
{'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
{'type': 'replication',
'numberOfIndividuals': 35900,
'ancestralGroups': [{'ancestralGroup': 'European'},
{'ancestralGroup': 'Hispanic or Latin American'},
{'ancestralGroup': 'African unspecified'}],
'countryOfOrigin': [{'majorArea': 'NR',
'region': 'NR',
'countryName': 'NR'}],
'countryOfRecruitment': [{'majorArea': 'Northern America',
'region': None,
'countryName': 'U.S.'},
{'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]}],
'diseaseTrait': {'trait': 'Ischemic stroke (cardioembolic)'},
'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
'replicationSampleSize': '579 European ancestry cases, 3,427 African unspecified, Hispanic and European ancestry cases, 18,515 European ancestry controls, 32,473 African unspecified, Hispanic and European ancestry controls',
'publicationInfo': {'pubmedId': '27068588',
'publicationDate': '2016-04-07',
'publication': 'Lancet Neurol',
'title': 'Identification of additional risk loci for stroke and small vessel disease: a meta-analysis of genome-wide association studies.',
'author': {'fullname': 'Chauhan G', 'orcid': None}}},
'pvalueDescription': None,
'orPerCopyNum': 1.4,
'snpType': 'known',
'multiSnpHaplotype': False,
'snpInteraction': False,
'pvalueMantissa': 1,
'pvalueExponent': -25,
'standardError': None,
'pvalue': 1e-25,
'betaNum': None,
'betaUnit': None,
'betaDirection': None,
'description': None,
'_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372'},
'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372{?projection}',
'templated': True},
'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372/snps'},
'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372/backgroundEfoTraits'},
'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372/study'},
'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/14964372/efoTraits'}}},
{'range': '[1.11-1.23]',
'snps': [{'rsId': 'rs7193343',
'merged': 0,
'functionalClass': 'intron_variant',
'lastUpdateDate': '2021-06-24T18:30:01.511+0000',
'locations': [{'chromosomeName': '16',
'chromosomePosition': 72995261,
'region': {'name': '16q22.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}}],
'genomicContexts': [{'isIntergenic': False,
'isUpstream': False,
'isDownstream': False,
'distance': 0,
'gene': {'geneName': 'ZFHX3',
'entrezGeneIds': [{'entrezGeneId': '463'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000140836'}]},
'location': {'chromosomeName': '16',
'chromosomePosition': 72995261,
'region': {'name': '16q22.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 97088,
'gene': {'geneName': 'HCCAT5',
'entrezGeneIds': [{'entrezGeneId': '283902'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000260880'}]},
'location': {'chromosomeName': '16',
'chromosomePosition': 72995261,
'region': {'name': '16q22.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}},
{'isIntergenic': False,
'isUpstream': False,
'isDownstream': False,
'distance': 0,
'gene': {'geneName': 'ZFHX3',
'entrezGeneIds': [{'entrezGeneId': '463'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000140836'}]},
'location': {'chromosomeName': '16',
'chromosomePosition': 72995261,
'region': {'name': '16q22.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 97088,
'gene': {'geneName': 'HCCAT5',
'entrezGeneIds': [{'entrezGeneId': '283902'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000260880'}]},
'location': {'chromosomeName': '16',
'chromosomePosition': 72995261,
'region': {'name': '16q22.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True}}}]}],
'loci': [{'haplotypeSnpCount': None,
'description': 'Single variant',
'strongestRiskAlleles': [{'riskAlleleName': 'rs7193343-T',
'riskFrequency': '0.174',
'genomeWide': False,
'limitedList': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7193343{?projection}',
'templated': True},
'proxySnps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/NR{?projection}',
'templated': True}}}],
'authorReportedGenes': [{'geneName': 'ZFHX3',
'entrezGeneIds': [{'entrezGeneId': '463'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000140836'}]}]}],
'riskFrequency': '0.174',
'study': {'initialSampleSize': 'up to 3,400 European ancestry cases, up to 208 African ancestry cases, up to 118 Hispanic cases, 26,690 European ancestry controls, 3,354 African ancestry controls, 2,429 Hispanic controls',
'gxe': False,
'gxg': False,
'snpCount': 15400000,
'qualifier': 'up to',
'imputed': True,
'pooled': False,
'studyDesignComment': None,
'accessionId': 'GCST003257',
'fullPvalueSet': False,
'userRequested': False,
'platforms': [{'manufacturer': 'Illumina'}],
'ancestries': [{'type': 'initial',
'numberOfIndividuals': 30090,
'ancestralGroups': [{'ancestralGroup': 'European'}],
'countryOfOrigin': [{'majorArea': 'NR',
'region': 'NR',
'countryName': 'NR'}],
'countryOfRecruitment': [{'majorArea': 'Europe',
'region': 'Northern Europe',
'countryName': 'Sweden'},
{'majorArea': 'Northern America', 'region': None, 'countryName': 'U.S.'},
{'majorArea': 'Europe',
'region': 'Eastern Europe',
'countryName': 'Poland'},
{'majorArea': 'Oceania',
'region': 'Australia/New Zealand',
'countryName': 'Australia'},
{'majorArea': 'Northern America',
'region': None,
'countryName': 'Canada'},
{'majorArea': 'Europe',
'region': 'Western Europe',
'countryName': 'Belgium'},
{'majorArea': 'Europe',
'region': 'Western Europe',
'countryName': 'Germany'},
{'majorArea': 'Europe',
'region': 'Northern Europe',
'countryName': 'U.K.'},
{'majorArea': 'Europe',
'region': 'Southern Europe',
'countryName': 'Spain'},
{'majorArea': 'Europe',
'region': 'Western Europe',
'countryName': 'Austria'},
{'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
{'type': 'replication',
'numberOfIndividuals': 3015,
'ancestralGroups': [{'ancestralGroup': 'African American or Afro-Caribbean'},
{'ancestralGroup': 'African unspecified'}],
'countryOfOrigin': [{'majorArea': 'NR',
'region': 'NR',
'countryName': 'NR'}],
'countryOfRecruitment': [{'majorArea': 'Northern America',
'region': None,
'countryName': 'U.S.'},
{'majorArea': 'NR', 'region': 'NR', 'countryName': 'NR'}]},
{'type': 'replication',
'numberOfIndividuals': 360,
'ancestralGroups': [{'ancestralGroup': 'East Asian'}],
'countryOfOrigin': [{'majorArea': 'NR',
'region': 'NR',
'countryName': 'NR'}],
'countryOfRecruitment': [{'majorArea': 'NR',
'region': 'NR',
'countryName': 'NR'}]},
{'type': 'replication',
'numberOfIndividuals': 277499,
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'templated': True}}}],
'genomicContexts': [{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 78716,
'gene': {'geneName': 'NPTX1',
'entrezGeneIds': [{'entrezGeneId': '4884'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000171246'}]},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 45990,
'gene': {'geneName': 'RPL31P7',
'entrezGeneIds': [{'entrezGeneId': '654391'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000232083'}]},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 45948,
'gene': {'geneName': 'RPL31P7',
'entrezGeneIds': [{'entrezGeneId': '654391'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000232083'}]},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 79952,
'gene': {'geneName': 'NPTX1',
'entrezGeneIds': [{'entrezGeneId': '4884'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000171246'}]},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': False,
'isDownstream': True,
'distance': 3543,
'gene': {'geneName': 'LOC105371922',
'entrezGeneIds': [{'entrezGeneId': '105371922'}],
'ensemblGeneIds': []},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
{'isIntergenic': False,
'isUpstream': False,
'isDownstream': False,
'distance': 0,
'gene': {'geneName': 'RPTOR',
'entrezGeneIds': [{'entrezGeneId': '57521'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000141564'}]},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 13904,
'gene': {'geneName': 'RPL32P31',
'entrezGeneIds': [{'entrezGeneId': '201259'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000213128'}]},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
{'isIntergenic': False,
'isUpstream': False,
'isDownstream': False,
'distance': 0,
'gene': {'geneName': 'RPTOR',
'entrezGeneIds': [{'entrezGeneId': '57521'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000141564'}]},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'NCBI',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
{'isIntergenic': True,
'isUpstream': True,
'isDownstream': False,
'distance': 13954,
'gene': {'geneName': 'RPL32P31',
'entrezGeneIds': [{'entrezGeneId': '201259'}],
'ensemblGeneIds': [{'ensemblGeneId': 'ENSG00000213128'}]},
'location': {'chromosomeName': '17',
'chromosomePosition': 80556559,
'region': {'name': '17q25.3'},
'_links': {'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}},
'source': 'Ensembl',
'mappingMethod': 'Ensembl_pipeline',
'isClosestGene': True,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}}]}],
'loci': [{'haplotypeSnpCount': None,
'description': 'Single variant',
'strongestRiskAlleles': [{'riskAlleleName': 'rs139293840-A',
'riskFrequency': None,
'genomeWide': False,
'limitedList': False,
'_links': {'snp': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs139293840{?projection}',
'templated': True}}}],
'authorReportedGenes': []}],
'riskFrequency': '0.01013',
'study': {'initialSampleSize': '497 Korean ancestry cases, 4,815 Korean ancestry controls',
'gxe': False,
'gxg': False,
'snpCount': 7975321,
'qualifier': None,
'imputed': True,
'pooled': False,
'studyDesignComment': None,
'accessionId': 'GCST90014127',
'fullPvalueSet': False,
'userRequested': False,
'platforms': [{'manufacturer': 'Affymetrix'}],
'ancestries': [{'type': 'initial',
'numberOfIndividuals': 5312,
'ancestralGroups': [{'ancestralGroup': 'East Asian'}],
'countryOfOrigin': [],
'countryOfRecruitment': [{'majorArea': 'Asia',
'region': 'Eastern Asia',
'countryName': 'Republic of Korea'}]}],
'diseaseTrait': {'trait': 'Cardio-cerebrovascular disease in diabetes mellitus'},
'genotypingTechnologies': [{'genotypingTechnology': 'Genome-wide genotyping array'}],
'replicationSampleSize': 'NA',
'publicationInfo': {'pubmedId': '33632238',
'publicationDate': '2021-02-25',
'publication': 'J Transl Med',
'title': 'Identification of susceptibility loci for cardiovascular disease in adults with hypertension, diabetes, and dyslipidemia.',
'author': {'fullname': 'Song Y', 'orcid': None}}},
'pvalueDescription': None,
'orPerCopyNum': 3.511,
'snpType': 'novel',
'multiSnpHaplotype': False,
'snpInteraction': False,
'pvalueMantissa': 2,
'pvalueExponent': -8,
'standardError': None,
'pvalue': 2e-08,
'betaNum': None,
'betaUnit': None,
'betaDirection': None,
'description': None,
'_links': {'self': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290'},
'association': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290{?projection}',
'templated': True},
'snps': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290/snps'},
'backgroundEfoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290/backgroundEfoTraits'},
'study': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290/study'},
'efoTraits': {'href': 'https://www.ebi.ac.uk/gwas/rest/api/associations/78852290/efoTraits'}}}]
In [3]:
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def gwascatalog_trait(efo):
base_url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/"+efo+"/associations?projection=associationByEfoTrait"
print("Start to retrieve data from GWASCatalog...")
print(" -Requesting GWAS associations through the following GWASCatalog API...")
print(" -api: "+ base_url)
# Perform POST request and check status code of response
r = requests.get(base_url)
if r.status_code == 200:
print(" -Retrieved data from GWASCatalog successffully ...")
print(" -Loading json ...")
# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
records=[]
sig_level = 5e-8
print(" -Parsing json ...")
records=list()
source="NCBI"
print("Number of associations:",len( api_response["_embedded"]["associations"]))
for association in api_response["_embedded"]["associations"]:
#association statistics:
p=float(association["pvalue"])
if p < sig_level:
try:
function_class=association["functionalClass"]
except:
function_class=None
try:
eaf=association["riskFrequency"]
except:
eaf= None
try:
study=association["study"]['publicationInfo']["title"]
pubmedid=association["study"]['publicationInfo']["pubmedId"]
except:
study= None
pubmedid = None
try:
gene = association["loci"][0]["authorReportedGenes"][0]["geneName"]
except:
gene = None
try:
OR=association["orPerCopyNum"]
except:
OR=None
try:
beta=association["betaNum"]
se=association["standardError"]
except:
beta=None
se=None
for snp in association["snps"]:
if len(snp["locations"])>0:
for record_num in range(len(snp["locations"])):
if snp["locations"][record_num]["chromosomeName"] in [str(i) for i in range(1,26)]+["x","X","y","Y","mt","MT"]:
if len(snp["genomicContexts"])>0:
closegenes=set()
distances=set()
ingene=set()
for gene_num in range(len(snp["genomicContexts"])):
if snp["genomicContexts"][gene_num]["source"]==source:
distance= str(snp["genomicContexts"][gene_num]["distance"])
ingene_name = snp["genomicContexts"][gene_num]["gene"]["geneName"]
if distance==0:
ingene.add(ingene_name)
continue
if snp["genomicContexts"][gene_num]["isClosestGene"] is True:
closegene_name = snp["genomicContexts"][gene_num]["gene"]["geneName"]
closegenes.add(closegene_name)
distances.add(distance)
if len(ingene)>0:
autogenes = ",".ingene
else:
autogenes = ",".join(closegenes)
row=[ snp["rsId"],
snp["locations"][record_num]["chromosomeName"],
snp["locations"][record_num]["chromosomePosition"],
gene,
autogenes,
function_class,
OR,
beta,
se,
p,
association["study"]["diseaseTrait"]["trait"],
study,
pubmedid
]
records.append(row)
#rsid locations
gwascatalog = pd.DataFrame(records,columns=["SNPID","CHR","POS","REPORT_GENENAME","CLOSEST_GENENAMES","FUNCTION_CLASS","OR","BETA","SE","P","TRAIT","STUDY","PUBMEDID"])
sigs = gl.Sumstats(gwascatalog,fmt="gwaslab",other=['REPORT_GENENAME', 'CLOSEST_GENENAMES','TRAIT', 'STUDY', 'PUBMEDID'],verbose=False)
sigs.fix_pos(verbose=False)
sigs.fix_chr(verbose=False)
sigs.sort_coordinate()
return sigs.data
def gwascatalog_trait(efo):
base_url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/"+efo+"/associations?projection=associationByEfoTrait"
print("Start to retrieve data from GWASCatalog...")
print(" -Requesting GWAS associations through the following GWASCatalog API...")
print(" -api: "+ base_url)
# Perform POST request and check status code of response
r = requests.get(base_url)
if r.status_code == 200:
print(" -Retrieved data from GWASCatalog successffully ...")
print(" -Loading json ...")
# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
records=[]
sig_level = 5e-8
print(" -Parsing json ...")
records=list()
source="NCBI"
print("Number of associations:",len( api_response["_embedded"]["associations"]))
for association in api_response["_embedded"]["associations"]:
#association statistics:
p=float(association["pvalue"])
if p < sig_level:
try:
function_class=association["functionalClass"]
except:
function_class=None
try:
eaf=association["riskFrequency"]
except:
eaf= None
try:
study=association["study"]['publicationInfo']["title"]
pubmedid=association["study"]['publicationInfo']["pubmedId"]
except:
study= None
pubmedid = None
try:
gene = association["loci"][0]["authorReportedGenes"][0]["geneName"]
except:
gene = None
try:
OR=association["orPerCopyNum"]
except:
OR=None
try:
beta=association["betaNum"]
se=association["standardError"]
except:
beta=None
se=None
for snp in association["snps"]:
if len(snp["locations"])>0:
for record_num in range(len(snp["locations"])):
if snp["locations"][record_num]["chromosomeName"] in [str(i) for i in range(1,26)]+["x","X","y","Y","mt","MT"]:
if len(snp["genomicContexts"])>0:
closegenes=set()
distances=set()
ingene=set()
for gene_num in range(len(snp["genomicContexts"])):
if snp["genomicContexts"][gene_num]["source"]==source:
distance= str(snp["genomicContexts"][gene_num]["distance"])
ingene_name = snp["genomicContexts"][gene_num]["gene"]["geneName"]
if distance==0:
ingene.add(ingene_name)
continue
if snp["genomicContexts"][gene_num]["isClosestGene"] is True:
closegene_name = snp["genomicContexts"][gene_num]["gene"]["geneName"]
closegenes.add(closegene_name)
distances.add(distance)
if len(ingene)>0:
autogenes = ",".ingene
else:
autogenes = ",".join(closegenes)
row=[ snp["rsId"],
snp["locations"][record_num]["chromosomeName"],
snp["locations"][record_num]["chromosomePosition"],
gene,
autogenes,
function_class,
OR,
beta,
se,
p,
association["study"]["diseaseTrait"]["trait"],
study,
pubmedid
]
records.append(row)
#rsid locations
gwascatalog = pd.DataFrame(records,columns=["SNPID","CHR","POS","REPORT_GENENAME","CLOSEST_GENENAMES","FUNCTION_CLASS","OR","BETA","SE","P","TRAIT","STUDY","PUBMEDID"])
sigs = gl.Sumstats(gwascatalog,fmt="gwaslab",other=['REPORT_GENENAME', 'CLOSEST_GENENAMES','TRAIT', 'STUDY', 'PUBMEDID'],verbose=False)
sigs.fix_pos(verbose=False)
sigs.fix_chr(verbose=False)
sigs.sort_coordinate()
return sigs.data
In [21]:
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known = gwascatalog_trait(efo="HP_0002140")
known = gwascatalog_trait(efo="HP_0002140")
Start to retrieve data from GWASCatalog... -Requesting GWAS associations through the following GWASCatalog API... -api: https://www.ebi.ac.uk/gwas/rest/api/efoTraits/HP_0002140/associations?projection=associationByEfoTrait -Retrieved data from GWASCatalog successffully ... -Loading json ... -Parsing json ... Number of associations: 429 Thu Oct 27 00:13:50 2022 Start to sort the genome coordinates... Thu Oct 27 00:13:50 2022 -Current Dataframe shape : 198 x 13 Thu Oct 27 00:13:50 2022 -Force converting POS to integers... Thu Oct 27 00:13:50 2022 -Sorting genome coordinates... Thu Oct 27 00:13:50 2022 Finished sorting genome coordinates successfully!
In [5]:
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known
known
Out[5]:
| SNPID | CHR | POS | BETA | SE | P | OR | STATUS | REPORT_GENENAME | CLOSEST_GENENAMES | TRAIT | STUDY | PUBMEDID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | rs880315 | 1 | 10736809 | NaN | NaN | 6.000000e-09 | NaN | 9990999 | CASZ1 | PEX14,LOC105376733 | Ischemic stroke | Multiancestry genome-wide association study of... | 29531354 |
| 1 | rs491203 | 1 | 15102737 | NaN | NaN | 8.000000e-09 | NaN | 9990999 | TMEM51 | TMEM51-AS1 | Acute ischemic stroke x type 2 diabetes intera... | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| 2 | rs138364069 | 1 | 50832533 | NaN | NaN | 7.000000e-09 | 3.570 | 9990999 | FAF1 | MRPS6P2,PHBP12 | Ischemic stroke (large artery atherosclerosis) | Genome-Wide Association Analysis of Young-Onse... | 26732560 |
| 3 | rs3176471 | 1 | 50973784 | NaN | NaN | 4.000000e-08 | 3.700 | 9990999 | CDKN2C | FAF1,MIR4421 | Ischemic stroke (large artery atherosclerosis) | Genome-Wide Association Analysis of Young-Onse... | 26732560 |
| 4 | rs1892534 | 1 | 65640261 | NaN | NaN | 2.000000e-16 | NaN | 9990999 | None | RN7SL854P,LOC100422694 | Ischemic stroke or fibrinogen levels (pleiotropy) | Multi-phenotype analyses of hemostatic traits ... | 35285134 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 193 | rs1800961 | 20 | 44413724 | NaN | NaN | 1.000000e-10 | NaN | 9990999 | None | MIR3646,LINC01430 | Ischemic stroke or fibrinogen levels (pleiotropy) | Multi-phenotype analyses of hemostatic traits ... | 35285134 |
| 194 | rs9808651 | 21 | 39094542 | NaN | NaN | 6.000000e-22 | NaN | 9990999 | None | RPL23AP12,LOC107985484 | Ischemic stroke or fibrinogen levels (pleiotropy) | Multi-phenotype analyses of hemostatic traits ... | 35285134 |
| 195 | rs5750823 | 22 | 39433968 | NaN | NaN | 1.000000e-12 | NaN | 9990999 | None | SYNGR1,MGAT3 | Ischemic stroke or von Willebrand factor level... | Multi-phenotype analyses of hemostatic traits ... | 35285134 |
| 196 | rs75347843 | 22 | 50673933 | NaN | NaN | 6.000000e-11 | NaN | 9990999 | None | ARSA,RNU6-409P | Ischemic stroke or fibrinogen levels (pleiotropy) | Multi-phenotype analyses of hemostatic traits ... | 35285134 |
| 197 | rs114209171 | 23 | 155050522 | NaN | NaN | 7.000000e-13 | 1.153 | 9990999 | F8 | F8,CMC4 | Thrombosis | Genome-wide association analysis of self-repor... | 26908601 |
198 rows × 13 columns
In [155]:
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!wget -O t2d_bbj.txt.gz http://jenger.riken.jp/14/
!wget -O t2d_bbj.txt.gz http://jenger.riken.jp/14/
--2022-10-26 23:54:33-- http://jenger.riken.jp/14/ Resolving jenger.riken.jp (jenger.riken.jp)... 134.160.84.25 Connecting to jenger.riken.jp (jenger.riken.jp)|134.160.84.25|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 274187574 (261M) [text/plain] Saving to: ‘t2d_bbj.txt.gz’ t2d_bbj.txt.gz 100%[===================>] 261.49M 11.1MB/s in 24s 2022-10-26 23:55:24 (10.8 MB/s) - ‘t2d_bbj.txt.gz’ saved [274187574/274187574]
In [4]:
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Thu Oct 27 00:58:00 2022 Start to initiate from file :t2d_bbj.txt.gz Thu Oct 27 00:58:01 2022 -Reading columns : POS,BETA,N,REF,P,ALT,SE,Frq,Dir,SNP,CHR Thu Oct 27 00:58:01 2022 -Renaming columns to : POS,BETA,N,NEA,P,EA,SE,EAF,DIRECTION,SNPID,CHR Thu Oct 27 00:58:01 2022 -Current dataframe shape : Rows 1000000 x 11 Columns Thu Oct 27 00:58:01 2022 -Initiating a status column ... Thu Oct 27 00:58:01 2022 -Reordering columns to : SNPID,CHR,POS,EA,NEA,EAF,BETA,SE,P,N,DIRECTION,STATUS Thu Oct 27 00:58:01 2022 -NEAF is specified... Thu Oct 27 00:58:01 2022 -Checking if 0<= NEAF <=1 ... Thu Oct 27 00:58:01 2022 -Converted NEAF to EAF. Thu Oct 27 00:58:01 2022 -Removed 0 variants with bad NEAF. Thu Oct 27 00:58:01 2022 Finished loading data successfully!
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Thu Oct 27 00:58:01 2022 Start to check IDs... Thu Oct 27 00:58:01 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 00:58:01 2022 -Checking if SNPID is chr:pos:ref:alt...(separator: - ,: , _) Thu Oct 27 00:58:03 2022 Finished checking IDs successfully! Thu Oct 27 00:58:03 2022 Start to fix chromosome notation... Thu Oct 27 00:58:03 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 00:58:05 2022 -All CHR are already fixed... Thu Oct 27 00:58:06 2022 Finished fixing chromosome notation successfully! Thu Oct 27 00:58:06 2022 Start to fix basepair positions... Thu Oct 27 00:58:06 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 00:58:07 2022 -Position upper_bound is: 250,000,000 Thu Oct 27 00:58:09 2022 -Remove outliers: 0 Thu Oct 27 00:58:09 2022 -Converted all position to datatype Int64. Thu Oct 27 00:58:09 2022 Finished fixing basepair position successfully! Thu Oct 27 00:58:09 2022 Start to fix alleles... Thu Oct 27 00:58:09 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 00:58:10 2022 -Converted all bases to string datatype and UPPERCASE. Thu Oct 27 00:58:11 2022 Finished fixing allele successfully! Thu Oct 27 00:58:11 2022 Start sanity check for statistics ... Thu Oct 27 00:58:11 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 00:58:11 2022 -Checking if N is Int64 and N>0 ... Thu Oct 27 00:58:11 2022 -Removed 0 variants with bad N. Thu Oct 27 00:58:11 2022 -Checking if 0<= EAF <=1 ... Thu Oct 27 00:58:11 2022 -Removed 0 variants with bad EAF. Thu Oct 27 00:58:11 2022 -Checking if MAC >=5 ... Thu Oct 27 00:58:11 2022 -Removed 0 variants with bad MAC. Thu Oct 27 00:58:11 2022 -Checking if 0< P <5e-300 ... Thu Oct 27 00:58:11 2022 -Removed 0 variants with bad P. Thu Oct 27 00:58:11 2022 -Checking if abs(BETA)<10 ... Thu Oct 27 00:58:11 2022 -Removed 0 variants with bad BETA. Thu Oct 27 00:58:11 2022 -Checking if SE >0 ... Thu Oct 27 00:58:11 2022 -Removed 0 variants with bad SE. Thu Oct 27 00:58:11 2022 -Checking STATUS... Thu Oct 27 00:58:12 2022 -Coverting STAUTUS to category. Thu Oct 27 00:58:12 2022 -Removed 0 variants with bad statistics in total. Thu Oct 27 00:58:12 2022 Finished sanity check successfully! Thu Oct 27 00:58:12 2022 Start to normalize variants... Thu Oct 27 00:58:12 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 00:58:12 2022 -No available variants to normalize.. Thu Oct 27 00:58:12 2022 Finished normalizing variants successfully!
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mysumstats.liftover(from_build="19",to_build="38",n_cores=4)
mysumstats.liftover(from_build="19",to_build="38",n_cores=4)
Thu Oct 27 00:58:12 2022 Start to perform liftover... Thu Oct 27 00:58:12 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 00:58:12 2022 -CPU Cores to use : 4 Thu Oct 27 00:58:12 2022 -Performing liftover ... Thu Oct 27 00:58:12 2022 -Creating converter : hg19 to hg38 Thu Oct 27 00:58:12 2022 -Converting variants with status code xxx0xxx :1000000... Thu Oct 27 00:59:23 2022 -Removed unmapped variants: 619 Thu Oct 27 00:59:28 2022 Finished liftover successfully!
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mysumstats.data
mysumstats.data
Out[7]:
| SNPID | CHR | POS | EA | NEA | EAF | BETA | SE | P | N | DIRECTION | STATUS | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1:725932_G_A | 1 | 790552 | G | A | 0.9960 | -0.0737 | 0.1394 | 0.59700 | 166718 | -?+- | 3860099 |
| 1 | 1:725933_A_G | 1 | 790553 | G | A | 0.0040 | 0.0737 | 0.1394 | 0.59730 | 166718 | +?-+ | 3860099 |
| 2 | 1:737801_T_C | 1 | 802421 | C | T | 0.0051 | 0.0490 | 0.1231 | 0.69080 | 166718 | +?-+ | 3860099 |
| 3 | 1:749963_T_TAA | 1 | 814583 | TAA | T | 0.8374 | 0.0213 | 0.0199 | 0.28460 | 166718 | -?++ | 3860399 |
| 4 | 1:751343_T_A | 1 | 815963 | T | A | 0.8593 | 0.0172 | 0.0156 | 0.27050 | 166718 | -?++ | 3860099 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 999995 | 2:6347639_C_A | 2 | 6207507 | C | A | 0.7900 | -0.0159 | 0.0111 | 0.15100 | 191764 | ---+ | 3860099 |
| 999996 | 2:6347694_G_C | 2 | 6207562 | G | C | 0.7907 | -0.0151 | 0.0111 | 0.17250 | 191764 | ---+ | 3860099 |
| 999997 | 2:6348478_G_A | 2 | 6208346 | G | A | 0.7860 | -0.0152 | 0.0111 | 0.17160 | 191764 | ---+ | 3860099 |
| 999998 | 2:6348490_G_C | 2 | 6208358 | G | C | 0.9985 | -0.3180 | 0.2032 | 0.11750 | 191764 | +--- | 3860099 |
| 999999 | 2:6348754_A_C | 2 | 6208622 | C | A | 0.1572 | 0.0297 | 0.0126 | 0.01846 | 191764 | +++- | 3860099 |
999381 rows × 12 columns
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known = gwascatalog_trait(efo="MONDO_0005148")
known = gwascatalog_trait(efo="MONDO_0005148")
Start to retrieve data from GWASCatalog... -Requesting GWAS associations through the following GWASCatalog API... -api: https://www.ebi.ac.uk/gwas/rest/api/efoTraits/MONDO_0005148/associations?projection=associationByEfoTrait -Retrieved data from GWASCatalog successffully ... -Loading json ... -Parsing json ... Number of associations: 5253 Thu Oct 27 00:35:03 2022 Start to sort the genome coordinates... Thu Oct 27 00:35:03 2022 -Current Dataframe shape : 3939 x 13 Thu Oct 27 00:35:03 2022 -Force converting POS to integers... Thu Oct 27 00:35:03 2022 -Sorting genome coordinates... Thu Oct 27 00:35:03 2022 Finished sorting genome coordinates successfully!
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known
known
Out[24]:
| SNPID | CHR | POS | BETA | SE | P | OR | STATUS | REPORT_GENENAME | CLOSEST_GENENAMES | TRAIT | STUDY | PUBMEDID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | rs12741141 | 1 | 6609910 | 0.0395 | 0.0048 | 1.000000e-16 | NaN | 9990999 | NR | KLHL21,PHF13 | Type 2 diabetes | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| 1 | rs11583755 | 1 | 6612669 | 0.0369 | 0.0041 | 1.000000e-19 | NaN | 9990999 | NR | KLHL21,PHF13 | Type 2 diabetes | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| 2 | rs1010447 | 1 | 11209739 | NaN | NaN | 2.000000e-08 | NaN | 9990999 | MTOR | RNU6-291P,ANGPTL7 | Body mass index and type 2 diabetes (pairwise) | Genome-wide discovery of genetic loci that unc... | 33619380 |
| 3 | rs4845987 | 1 | 11246222 | 0.0282 | 0.0051 | 3.000000e-08 | NaN | 9990999 | NR | RPL39P6,UBIAD1 | Type 2 diabetes | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| 4 | rs7554251 | 1 | 11257875 | 0.0297 | 0.0045 | 3.000000e-11 | NaN | 9990999 | NR | RPL39P6,UBIAD1 | Type 2 diabetes | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 3934 | rs5945326 | 23 | 153634467 | NaN | NaN | 2.000000e-12 | 1.140000 | 9990999 | DUSP9 | LOC105373384,DUSP9 | Type 2 diabetes | Genome-wide association study identifies three... | 23945395 |
| 3935 | rs5945326 | 23 | 153634467 | NaN | NaN | 3.000000e-10 | 1.270000 | 9990999 | DUSP9 | LOC105373384,DUSP9 | Type 2 diabetes | Twelve type 2 diabetes susceptibility loci ide... | 20581827 |
| 3936 | rs5945326 | 23 | 153634467 | 0.1203 | 0.0055 | 8.000000e-106 | NaN | 9990999 | None | LOC105373384,DUSP9 | Type 2 diabetes | A cross-population atlas of genetic associatio... | 34594039 |
| 3937 | rs1894299 | 23 | 153643433 | NaN | NaN | 9.000000e-58 | 1.130000 | 9990999 | DUSP9 | LOC105373384,RPL18AP16 | Type 2 diabetes | Identification of 28 new susceptibility loci f... | 30718926 |
| 3938 | rs1894299 | 23 | 153643433 | NaN | NaN | 2.000000e-67 | 0.884338 | 9990999 | None | LOC105373384,RPL18AP16 | Type 2 diabetes | Large-scale genome-wide association study in a... | 32514122 |
3939 rows × 13 columns
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known.to_csv("t2d_known.txt",index=None)
known.to_csv("t2d_known.txt",index=None)
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import requests
import json
import pandas as pd
import sys
sys.path.insert(0,"/home/yunye/gwaslab/gwaslab/src")
import gwaslab as gl
import requests
import json
import pandas as pd
import sys
sys.path.insert(0,"/home/yunye/gwaslab/gwaslab/src")
import gwaslab as gl
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mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
snpid="SNP",
chrom="CHR",
pos="POS",
ea="ALT",
nea="REF",
neaf="Frq",
beta="BETA",
se="SE",
p="P",
direction="Dir",
n="N",nrows=1000000)
mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
snpid="SNP",
chrom="CHR",
pos="POS",
ea="ALT",
nea="REF",
neaf="Frq",
beta="BETA",
se="SE",
p="P",
direction="Dir",
n="N",nrows=1000000)
Thu Oct 27 01:33:16 2022 Start to initiate from file :t2d_bbj.txt.gz Thu Oct 27 01:33:17 2022 -Reading columns : CHR,REF,P,POS,SE,BETA,ALT,SNP,Dir,Frq,N Thu Oct 27 01:33:17 2022 -Renaming columns to : CHR,NEA,P,POS,SE,BETA,EA,SNPID,DIRECTION,EAF,N Thu Oct 27 01:33:17 2022 -Current dataframe shape : Rows 1000000 x 11 Columns Thu Oct 27 01:33:17 2022 -Initiating a status column ... Thu Oct 27 01:33:17 2022 -Reordering columns to : SNPID,CHR,POS,EA,NEA,EAF,BETA,SE,P,N,DIRECTION,STATUS Thu Oct 27 01:33:18 2022 -NEAF is specified... Thu Oct 27 01:33:18 2022 -Checking if 0<= NEAF <=1 ... Thu Oct 27 01:33:18 2022 -Converted NEAF to EAF. Thu Oct 27 01:33:18 2022 -Removed 0 variants with bad NEAF. Thu Oct 27 01:33:18 2022 Finished loading data successfully!
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mysumstats.basic_check()
mysumstats.basic_check()
Thu Oct 27 01:33:18 2022 Start to check IDs... Thu Oct 27 01:33:18 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 01:33:18 2022 -Checking if SNPID is chr:pos:ref:alt...(separator: - ,: , _) Thu Oct 27 01:33:19 2022 Finished checking IDs successfully! Thu Oct 27 01:33:19 2022 Start to fix chromosome notation... Thu Oct 27 01:33:19 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 01:33:21 2022 -All CHR are already fixed... Thu Oct 27 01:33:23 2022 Finished fixing chromosome notation successfully! Thu Oct 27 01:33:23 2022 Start to fix basepair positions... Thu Oct 27 01:33:23 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 01:33:24 2022 -Position upper_bound is: 250,000,000 Thu Oct 27 01:33:25 2022 -Remove outliers: 0 Thu Oct 27 01:33:26 2022 -Converted all position to datatype Int64. Thu Oct 27 01:33:26 2022 Finished fixing basepair position successfully! Thu Oct 27 01:33:26 2022 Start to fix alleles... Thu Oct 27 01:33:26 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 01:33:26 2022 -Converted all bases to string datatype and UPPERCASE. Thu Oct 27 01:33:27 2022 Finished fixing allele successfully! Thu Oct 27 01:33:27 2022 Start sanity check for statistics ... Thu Oct 27 01:33:27 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 01:33:27 2022 -Checking if N is Int64 and N>0 ... Thu Oct 27 01:33:27 2022 -Removed 0 variants with bad N. Thu Oct 27 01:33:27 2022 -Checking if 0<= EAF <=1 ... Thu Oct 27 01:33:27 2022 -Removed 0 variants with bad EAF. Thu Oct 27 01:33:27 2022 -Checking if MAC >=5 ... Thu Oct 27 01:33:27 2022 -Removed 0 variants with bad MAC. Thu Oct 27 01:33:27 2022 -Checking if 0< P <5e-300 ... Thu Oct 27 01:33:28 2022 -Removed 0 variants with bad P. Thu Oct 27 01:33:28 2022 -Checking if abs(BETA)<10 ... Thu Oct 27 01:33:28 2022 -Removed 0 variants with bad BETA. Thu Oct 27 01:33:28 2022 -Checking if SE >0 ... Thu Oct 27 01:33:28 2022 -Removed 0 variants with bad SE. Thu Oct 27 01:33:28 2022 -Checking STATUS... Thu Oct 27 01:33:28 2022 -Coverting STAUTUS to category. Thu Oct 27 01:33:28 2022 -Removed 0 variants with bad statistics in total. Thu Oct 27 01:33:28 2022 Finished sanity check successfully! Thu Oct 27 01:33:28 2022 Start to normalize variants... Thu Oct 27 01:33:28 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 01:33:29 2022 -No available variants to normalize.. Thu Oct 27 01:33:29 2022 Finished normalizing variants successfully!
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mysumstats.liftover(from_build="19",to_build="38",n_cores=4)
mysumstats.liftover(from_build="19",to_build="38",n_cores=4)
Thu Oct 27 01:34:28 2022 Start to perform liftover... Thu Oct 27 01:34:28 2022 -Current Dataframe shape : 1000000 x 12 Thu Oct 27 01:34:28 2022 -CPU Cores to use : 4 Thu Oct 27 01:34:28 2022 -Performing liftover ... Thu Oct 27 01:34:28 2022 -Creating converter : hg19 to hg38 Thu Oct 27 01:34:29 2022 -Converting variants with status code xxx0xxx :1000000... Thu Oct 27 01:35:39 2022 -Removed unmapped variants: 619 Thu Oct 27 01:35:45 2022 Finished liftover successfully!
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known = pd.read_csv("t2d_known.txt")
known = pd.read_csv("t2d_known.txt")
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known
known
Out[5]:
| SNPID | CHR | POS | BETA | SE | P | OR | STATUS | REPORT_GENENAME | CLOSEST_GENENAMES | TRAIT | STUDY | PUBMEDID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | rs12741141 | 1 | 6609910 | 0.0395 | 0.0048 | 1.000000e-16 | NaN | 9990999 | NR | KLHL21,PHF13 | Type 2 diabetes | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| 1 | rs11583755 | 1 | 6612669 | 0.0369 | 0.0041 | 1.000000e-19 | NaN | 9990999 | NR | KLHL21,PHF13 | Type 2 diabetes | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| 2 | rs1010447 | 1 | 11209739 | NaN | NaN | 2.000000e-08 | NaN | 9990999 | MTOR | RNU6-291P,ANGPTL7 | Body mass index and type 2 diabetes (pairwise) | Genome-wide discovery of genetic loci that unc... | 33619380 |
| 3 | rs4845987 | 1 | 11246222 | 0.0282 | 0.0051 | 3.000000e-08 | NaN | 9990999 | NR | RPL39P6,UBIAD1 | Type 2 diabetes | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| 4 | rs7554251 | 1 | 11257875 | 0.0297 | 0.0045 | 3.000000e-11 | NaN | 9990999 | NR | RPL39P6,UBIAD1 | Type 2 diabetes | Discovery of 318 new risk loci for type 2 diab... | 32541925 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 3934 | rs5945326 | 23 | 153634467 | NaN | NaN | 2.000000e-12 | 1.140000 | 9990999 | DUSP9 | LOC105373384,DUSP9 | Type 2 diabetes | Genome-wide association study identifies three... | 23945395 |
| 3935 | rs5945326 | 23 | 153634467 | NaN | NaN | 3.000000e-10 | 1.270000 | 9990999 | DUSP9 | LOC105373384,DUSP9 | Type 2 diabetes | Twelve type 2 diabetes susceptibility loci ide... | 20581827 |
| 3936 | rs5945326 | 23 | 153634467 | 0.1203 | 0.0055 | 8.000000e-106 | NaN | 9990999 | NaN | LOC105373384,DUSP9 | Type 2 diabetes | A cross-population atlas of genetic associatio... | 34594039 |
| 3937 | rs1894299 | 23 | 153643433 | NaN | NaN | 9.000000e-58 | 1.130000 | 9990999 | DUSP9 | LOC105373384,RPL18AP16 | Type 2 diabetes | Identification of 28 new susceptibility loci f... | 30718926 |
| 3938 | rs1894299 | 23 | 153643433 | NaN | NaN | 2.000000e-67 | 0.884338 | 9990999 | NaN | LOC105373384,RPL18AP16 | Type 2 diabetes | Large-scale genome-wide association study in a... | 32514122 |
3939 rows × 13 columns
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mysumstats.get_novel(known = known,only_novel=False)
mysumstats.get_novel(known = known,only_novel=False)
Thu Oct 27 01:35:53 2022 Start to extract lead variants... Thu Oct 27 01:35:53 2022 -Processing 999381 variants... Thu Oct 27 01:35:53 2022 -Significance threshold : 5e-08 Thu Oct 27 01:35:53 2022 -Sliding window size: 500 kb Thu Oct 27 01:35:54 2022 -Found 543 significant variants in total... Thu Oct 27 01:35:54 2022 -Identified 4 lead variants! Thu Oct 27 01:35:54 2022 Finished extracting lead variants successfully! Thu Oct 27 01:35:54 2022 Start to check if lead variants are known... Thu Oct 27 01:35:54 2022 -Lead variants in known loci: 3939 Thu Oct 27 01:35:54 2022 -Checking the minimum distance between identified lead variants and provided known variants... Thu Oct 27 01:35:54 2022 -Identified 4 known vairants in current sumstats... Thu Oct 27 01:35:54 2022 -Identified 0 novel vairants in current sumstats... Thu Oct 27 01:35:54 2022 Finished checking known or novel successfully!
Out[9]:
| SNPID | CHR | POS | EA | NEA | EAF | BETA | SE | P | N | DIRECTION | STATUS | TCHR+POS | DISTANCE_TO_KNOWN | KNOWN_ID | NOVEL | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 96739 | 1:22068326_A_G | 1 | 21741833 | G | A | 0.7550 | 0.0621 | 0.0103 | 1.629000e-09 | 191764 | ++++ | 3860099 | 1021741833 | 0 | rs1825307 | False |
| 213860 | 1:51103268_T_C | 1 | 50637596 | C | T | 0.7953 | -0.0802 | 0.0120 | 2.519000e-11 | 191764 | ---- | 3860099 | 1050637596 | 0 | rs12031188 | False |
| 534095 | 1:154309595_TA_T | 1 | 154337119 | TA | T | 0.0947 | -0.0915 | 0.0166 | 3.289000e-08 | 191764 | ---- | 3860399 | 1154337119 | 1 | rs68062313 | False |
| 969974 | 2:640986_CACAT_C | 2 | 640986 | C | CACAT | 0.9006 | -0.0946 | 0.0150 | 2.665000e-10 | 191764 | ---- | 3860399 | 2000640986 | 1 | rs72156956 | False |
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gwascatalog = pd.DataFrame(records,columns=["SNPID","CHR","POS","REPORT_GENENAME","CLOSEST_GENENAMES","FUNCTION_CLASS","OR","BETA","SE","P","TRAIT","STUDY","PUBMEDID"])
sigs = gl.Sumstats(gwascatalog,fmt="gwaslab",other=['REPORT_GENENAME', 'CLOSEST_GENENAMES','TRAIT', 'STUDY', 'PUBMEDID'],verbose=False)
sigs.fix_pos(verbose=False)
sigs.fix_chr(verbose=False)
gwascatalog = pd.DataFrame(records,columns=["SNPID","CHR","POS","REPORT_GENENAME","CLOSEST_GENENAMES","FUNCTION_CLASS","OR","BETA","SE","P","TRAIT","STUDY","PUBMEDID"])
sigs = gl.Sumstats(gwascatalog,fmt="gwaslab",other=['REPORT_GENENAME', 'CLOSEST_GENENAMES','TRAIT', 'STUDY', 'PUBMEDID'],verbose=False)
sigs.fix_pos(verbose=False)
sigs.fix_chr(verbose=False)
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sigs.data
sigs.data
Out[147]:
| SNPID | CHR | POS | BETA | SE | P | OR | STATUS | REPORT_GENENAME | CLOSEST_GENENAMES | TRAIT | STUDY | PUBMEDID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | rs75021220 | 4 | 110737238 | NaN | NaN | 1.000000e-25 | 1.400 | 9990999 | PITX2 | PITX2 | Ischemic stroke (cardioembolic) | Identification of additional risk loci for str... | 27068588 |
| 1 | rs7193343 | 16 | 72995261 | NaN | NaN | 2.000000e-10 | 1.170 | 9990999 | ZFHX3 | HCCAT5 | Ischemic stroke (cardioembolic) | Loci associated with ischaemic stroke and its ... | 26708676 |
| 2 | rs2200733 | 4 | 110789013 | NaN | NaN | 3.000000e-32 | 1.370 | 9990999 | PITX2 | PITX2,MIR297 | Ischemic stroke (cardioembolic) | Loci associated with ischaemic stroke and its ... | 26708676 |
| 3 | rs74475935 | 16 | 15961249 | NaN | NaN | 5.000000e-11 | 4.630 | 9990999 | ABCC1 | LOC107984869 | Ischemic stroke (undetermined subtype) | Loci associated with ischaemic stroke and its ... | 26708676 |
| 4 | rs10744777 | 12 | 111795214 | NaN | NaN | 3.000000e-09 | 1.170 | 9990999 | ALDH2 | MIR6761,ACAD10 | Ischemic stroke (small artery occlusion) | Loci associated with ischaemic stroke and its ... | 26708676 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 193 | rs11880613 | 19 | 10793296 | 0.0613 | 0.011 | 3.000000e-08 | NaN | 9990999 | None | MIR4748,MIR199A1 | Ischemic stroke | A cross-population atlas of genetic associatio... | 34594039 |
| 194 | rs3897976 | 3 | 41565201 | NaN | NaN | 3.000000e-08 | 2.162 | 9990999 | None | ALCAM | Ischemic stroke in dyslipidemia | Identification of susceptibility loci for card... | 33632238 |
| 195 | rs149608518 | 4 | 164551523 | NaN | NaN | 1.000000e-08 | 5.587 | 9990999 | None | RNU6-284P | Ischemic stroke in diabetes mellitus | Identification of susceptibility loci for card... | 33632238 |
| 196 | rs189668056 | 2 | 38081685 | NaN | NaN | 4.000000e-08 | 2.027 | 9990999 | None | CYP1B1,LOC105374466 | Cardio-cerebrovascular disease in dyslipidemia | Identification of susceptibility loci for card... | 33632238 |
| 197 | rs139293840 | 17 | 80556559 | NaN | NaN | 2.000000e-08 | 3.511 | 9990999 | None | RPL32P31,LOC105371922 | Cardio-cerebrovascular disease in diabetes mel... | Identification of susceptibility loci for card... | 33632238 |
198 rows × 13 columns
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locations = pd.json_normalize(api_response["_embedded"]["associations"],"snps",errors='ignore')[["locations","genomicContexts"]]
locations = pd.json_normalize(api_response["_embedded"]["associations"],"snps",errors='ignore')[["locations","genomicContexts"]]
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Out[135]:
| locations | genomicContexts | |
|---|---|---|
| 0 | [{'chromosomeName': '8', 'chromosomePosition':... | [{'isIntergenic': False, 'isUpstream': False, ... |
| 1 | [{'chromosomeName': '19', 'chromosomePosition'... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 2 | [{'chromosomeName': '8', 'chromosomePosition':... | [{'isIntergenic': True, 'isUpstream': False, '... |
| 3 | [{'chromosomeName': '11', 'chromosomePosition'... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 4 | [{'chromosomeName': '1', 'chromosomePosition':... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| ... | ... | ... |
| 68 | [{'chromosomeName': '19', 'chromosomePosition'... | [{'isIntergenic': True, 'isUpstream': False, '... |
| 69 | [{'chromosomeName': '3', 'chromosomePosition':... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 70 | [{'chromosomeName': '19', 'chromosomePosition'... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 71 | [{'chromosomeName': 'CHR_HSCHR6_MHC_DBB_CTG1',... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 72 | [{'chromosomeName': 'CHR_HSCHR6_MHC_MCF_CTG1',... | [{'isIntergenic': True, 'isUpstream': False, '... |
73 rows × 2 columns
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layer1 = pd.json_normalize(api_response["_embedded"]["associations"])
layer1
layer1 = pd.json_normalize(api_response["_embedded"]["associations"])
layer1
Out[77]:
| range | snps | loci | riskFrequency | pvalueDescription | orPerCopyNum | snpType | multiSnpHaplotype | snpInteraction | pvalueMantissa | ... | study.publicationInfo.title | study.publicationInfo.author.fullname | study.publicationInfo.author.orcid | _links.self.href | _links.association.href | _links.association.templated | _links.snps.href | _links.backgroundEfoTraits.href | _links.study.href | _links.efoTraits.href | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | [1.65-2.5] | [{'rsId': 'rs12678747', 'merged': 0, 'function... | [{'haplotypeSnpCount': None, 'description': 'S... | NR | None | 2.03 | novel | False | False | 3 | ... | Genome-Wide association between EYA1 and Aspir... | Bourgeois S | None | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| 1 | NR | [{'rsId': 'rs681343', 'merged': 0, 'functional... | [{'haplotypeSnpCount': None, 'description': 'S... | 0.49 | None | 0.92 | novel | False | False | 2 | ... | GWAS of peptic ulcer disease implicates Helico... | Wu Y | 0000-0002-5977-1526 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| 2 | NR | [{'rsId': 'rs2976388', 'merged': 0, 'functiona... | [{'haplotypeSnpCount': None, 'description': 'S... | 0.58 | None | 1.09 | novel | False | False | 2 | ... | GWAS of peptic ulcer disease implicates Helico... | Wu Y | 0000-0002-5977-1526 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| 3 | NR | [{'rsId': 'rs10500661', 'merged': 0, 'function... | [{'haplotypeSnpCount': None, 'description': 'S... | 0.8 | None | 0.90 | novel | False | False | 4 | ... | GWAS of peptic ulcer disease implicates Helico... | Wu Y | 0000-0002-5977-1526 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| 4 | NR | [{'rsId': 'rs147048677', 'merged': 0, 'functio... | [{'haplotypeSnpCount': None, 'description': 'S... | 0.94 | None | 0.86 | novel | False | False | 9 | ... | GWAS of peptic ulcer disease implicates Helico... | Wu Y | 0000-0002-5977-1526 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 68 | None | [{'rsId': 'rs11083749', 'merged': 0, 'function... | [{'haplotypeSnpCount': None, 'description': 'S... | NR | None | NaN | novel | False | False | 3 | ... | A large-scale genome-wide cross-trait analysis... | Adewuyi EO | 0000-0002-4533-0340 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| 69 | None | [{'rsId': 'rs709210', 'merged': 0, 'functional... | [{'haplotypeSnpCount': None, 'description': 'S... | NR | None | NaN | novel | False | False | 4 | ... | A large-scale genome-wide cross-trait analysis... | Adewuyi EO | 0000-0002-4533-0340 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| 70 | None | [{'rsId': 'rs11880948', 'merged': 0, 'function... | [{'haplotypeSnpCount': None, 'description': 'S... | NR | None | NaN | novel | False | False | 6 | ... | A large-scale genome-wide cross-trait analysis... | Adewuyi EO | 0000-0002-4533-0340 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| 71 | None | [{'rsId': 'rs28732222', 'merged': 0, 'function... | [{'haplotypeSnpCount': None, 'description': 'S... | NR | None | NaN | novel | False | False | 1 | ... | A large-scale genome-wide cross-trait analysis... | Adewuyi EO | 0000-0002-4533-0340 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
| 72 | None | [{'rsId': 'rs17206350', 'merged': 0, 'function... | [{'haplotypeSnpCount': None, 'description': 'S... | NR | None | NaN | novel | False | False | 1 | ... | A large-scale genome-wide cross-trait analysis... | Adewuyi EO | 0000-0002-4533-0340 | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | True | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... | https://www.ebi.ac.uk/gwas/rest/api/associatio... |
73 rows × 46 columns
In [78]:
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layer2 = pd.json_normalize(api_response["_embedded"]["associations"],"snps")
layer2
layer2 = pd.json_normalize(api_response["_embedded"]["associations"],"snps")
layer2
Out[78]:
| rsId | merged | functionalClass | lastUpdateDate | locations | genomicContexts | |
|---|---|---|---|---|---|---|
| 0 | rs12678747 | 0 | intron_variant | 2022-03-23T17:19:52.947+0000 | [{'chromosomeName': '8', 'chromosomePosition':... | [{'isIntergenic': False, 'isUpstream': False, ... |
| 1 | rs681343 | 0 | stop_gained | 2022-08-03T16:59:51.731+0000 | [{'chromosomeName': '19', 'chromosomePosition'... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 2 | rs2976388 | 0 | intron_variant | 2021-06-24T21:12:27.021+0000 | [{'chromosomeName': '8', 'chromosomePosition':... | [{'isIntergenic': True, 'isUpstream': False, '... |
| 3 | rs10500661 | 0 | intergenic_variant | 2021-06-25T04:18:24.804+0000 | [{'chromosomeName': '11', 'chromosomePosition'... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 4 | rs147048677 | 0 | synonymous_variant | 2021-06-24T21:12:28.862+0000 | [{'chromosomeName': '1', 'chromosomePosition':... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| ... | ... | ... | ... | ... | ... | ... |
| 68 | rs11083749 | 0 | intron_variant | 2022-09-09T17:04:12.767+0000 | [{'chromosomeName': '19', 'chromosomePosition'... | [{'isIntergenic': True, 'isUpstream': False, '... |
| 69 | rs709210 | 0 | missense_variant | 2022-09-09T17:04:14.640+0000 | [{'chromosomeName': '3', 'chromosomePosition':... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 70 | rs11880948 | 0 | intron_variant | 2022-09-09T17:04:14.970+0000 | [{'chromosomeName': '19', 'chromosomePosition'... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 71 | rs28732222 | 0 | downstream_gene_variant | 2022-09-09T17:04:19.712+0000 | [{'chromosomeName': 'CHR_HSCHR6_MHC_DBB_CTG1',... | [{'isIntergenic': True, 'isUpstream': True, 'i... |
| 72 | rs17206350 | 0 | upstream_gene_variant | 2022-09-09T17:04:24.164+0000 | [{'chromosomeName': 'CHR_HSCHR6_MHC_MCF_CTG1',... | [{'isIntergenic': True, 'isUpstream': False, '... |
73 rows × 6 columns
In [80]:
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layer3 = pd.json_normalize(api_response["_embedded"]["associations"],["snps","locations"])
layer3
layer3 = pd.json_normalize(api_response["_embedded"]["associations"],["snps","locations"])
layer3
Out[80]:
| chromosomeName | chromosomePosition | region.name | _links.snps | _links.snps.href | _links.snps.templated | |
|---|---|---|---|---|---|---|
| 0 | 8 | 71202541 | 8q13.3 | [{'href': 'https://www.ebi.ac.uk/gwas/rest/api... | NaN | NaN |
| 1 | 8 | 71202541 | 8q13.3 | [{'href': 'https://www.ebi.ac.uk/gwas/rest/api... | NaN | NaN |
| 2 | 19 | 48703205 | 19q13.33 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 3 | 8 | 142678838 | 8q24.3 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 4 | 11 | 6252514 | 11p15.4 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| ... | ... | ... | ... | ... | ... | ... |
| 107 | 6 | 32707290 | 6p21.32 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 108 | CHR_HSCHR6_MHC_DBB_CTG1 | 32686300 | None | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 109 | CHR_HSCHR6_MHC_COX_CTG1 | 32630720 | None | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 110 | CHR_HSCHR6_MHC_QBL_CTG1 | 32635972 | None | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 111 | CHR_HSCHR6_MHC_SSTO_CTG1 | 32799385 | None | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
112 rows × 6 columns
In [82]:
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layer3.drop_duplicates(subset=["chromosomeName","chromosomePosition"])
layer3.drop_duplicates(subset=["chromosomeName","chromosomePosition"])
Out[82]:
| chromosomeName | chromosomePosition | region.name | _links.snps | _links.snps.href | _links.snps.templated | |
|---|---|---|---|---|---|---|
| 0 | 8 | 71202541 | 8q13.3 | [{'href': 'https://www.ebi.ac.uk/gwas/rest/api... | NaN | NaN |
| 2 | 19 | 48703205 | 19q13.33 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 3 | 8 | 142678838 | 8q24.3 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 4 | 11 | 6252514 | 11p15.4 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 5 | 1 | 155192003 | 1q22 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| ... | ... | ... | ... | ... | ... | ... |
| 107 | 6 | 32707290 | 6p21.32 | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 108 | CHR_HSCHR6_MHC_DBB_CTG1 | 32686300 | None | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 109 | CHR_HSCHR6_MHC_COX_CTG1 | 32630720 | None | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 110 | CHR_HSCHR6_MHC_QBL_CTG1 | 32635972 | None | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
| 111 | CHR_HSCHR6_MHC_SSTO_CTG1 | 32799385 | None | NaN | https://www.ebi.ac.uk/gwas/rest/api/singleNucl... | True |
109 rows × 6 columns
In [41]:
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for i in api_response["_embedded"]["associations"]:
if "pvalue" in i:
if float(i["pvalue"])<5e-8:
snp = pd.json_normalize(api_response["_embedded"]["associations"][0]["snps"],max_level=0)
if "rsId" in i["snps"][0]:
print(i["snps"][0]["rsId"], end=",")
if "locations" in i["snps"][0]:
if len(i["snps"][0]["locations"])>0:
print(i["snps"][0]["locations"][0]["chromosomeName"],end=" ")
if len(i["snps"][0]["locations"])>0:
print(i["snps"][0]["locations"][0]["chromosomePosition"],end=" ")
if "genomicContexts" in i["snps"][0]:
if "gene" in i["snps"][0]["genomicContexts"][0]:
if "geneName" in i["snps"][0]["genomicContexts"][0]["gene"]:
print(i["snps"][0]["genomicContexts"][0]["gene"]["geneName"])
print(i["pvalue"])
for i in api_response["_embedded"]["associations"]:
if "pvalue" in i:
if float(i["pvalue"])<5e-8:
snp = pd.json_normalize(api_response["_embedded"]["associations"][0]["snps"],max_level=0)
if "rsId" in i["snps"][0]:
print(i["snps"][0]["rsId"], end=",")
if "locations" in i["snps"][0]:
if len(i["snps"][0]["locations"])>0:
print(i["snps"][0]["locations"][0]["chromosomeName"],end=" ")
if len(i["snps"][0]["locations"])>0:
print(i["snps"][0]["locations"][0]["chromosomePosition"],end=" ")
if "genomicContexts" in i["snps"][0]:
if "gene" in i["snps"][0]["genomicContexts"][0]:
if "geneName" in i["snps"][0]["genomicContexts"][0]["gene"]:
print(i["snps"][0]["genomicContexts"][0]["gene"]["geneName"])
print(i["pvalue"])
rs12678747,8 71202541 EYA1 3e-11 rs681343,19 48703205 FAM83E 2e-15 rs2976388,8 142678838 SLURP2 2e-14 rs10500661,11 6252514 OR52B2 4e-14 rs147048677,1 155192003 HMGN2P18 9e-12 rs78459074,CHR_HSCHR11_2_CTG1 1036727 AP2A2 3e-10 rs34074411,17 41710996 GAST 3e-10 rs687621,9 133261662 MED22 1e-09 rs9581957,13 27983752 CDX2 4e-09 rs200964,6 27899165 H4C11 3.0000000000000003e-13 rs967823,17 52239916 CA10 2e-12 chr19:18793695,
--------------------------------------------------------------------------- IndexError Traceback (most recent call last) <ipython-input-41-786e8dc656a6> in <module> 10 print(i["snps"][0]["locations"][0]["chromosomePosition"],end=" ") 11 if "genomicContexts" in i["snps"][0]: ---> 12 if "gene" in i["snps"][0]["genomicContexts"][0]: 13 if "geneName" in i["snps"][0]["genomicContexts"][0]["gene"]: 14 print(i["snps"][0]["genomicContexts"][0]["gene"]["geneName"]) IndexError: list index out of range
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for item,associations in api_response["_embedded"].items():
associations[0]["snp"][0]["rsID"]
for item,associations in api_response["_embedded"].items():
associations[0]["snp"][0]["rsID"]
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In [48]:
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import re
pattern = re.compile(r'rs[0-9]+')
import re
pattern = re.compile(r'rs[0-9]+')
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a=pattern.search("'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs17206350{?projection}'")
a[0]
a=pattern.search("'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs17206350{?projection}'")
a[0]
rs17206350
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for value in api_response["_embedded"].values():
for i in value:
a=pattern.search(i['loci'][0]["strongestRiskAlleles"][0]["_links"]["snp"]["href"])
if a is None:
continue
base_url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/"+a[0]
r = requests.get(base_url)
snp_response = json.loads(r.text)
print(a[0],snp_response["locations"][0]["chromosomeName"],api_response["locations"][0]["chromosomePosition"])
for value in api_response["_embedded"].values():
for i in value:
a=pattern.search(i['loci'][0]["strongestRiskAlleles"][0]["_links"]["snp"]["href"])
if a is None:
continue
base_url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/"+a[0]
r = requests.get(base_url)
snp_response = json.loads(r.text)
print(a[0],snp_response["locations"][0]["chromosomeName"],api_response["locations"][0]["chromosomePosition"])
--------------------------------------------------------------------------- KeyError Traceback (most recent call last) <ipython-input-55-257d03c020b1> in <module> ----> 1 for value in api_response["_embedded"].values(): 2 for i in value: 3 a=pattern.search(i['loci'][0]["strongestRiskAlleles"][0]["_links"]["snp"]["href"]) 4 if a is None: 5 continue KeyError: '_embedded'
In [40]:
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base_url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs3852865"
# Perform POST request and check status code of response
r = requests.get(base_url)
print(r.status_code)
# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
print(api_response["locations"][0]["chromosomeName"],api_response["locations"][0]["chromosomePosition"])
base_url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs3852865"
# Perform POST request and check status code of response
r = requests.get(base_url)
print(r.status_code)
# Transform API response from JSON into Python dictionary and print in console
api_response = json.loads(r.text)
print(api_response["locations"][0]["chromosomeName"],api_response["locations"][0]["chromosomePosition"])
200 19 51210809
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